[phenixbb] following on the anomalous map

CPMAS Chen cpmasmit at gmail.com
Tue Aug 26 06:49:54 PDT 2014

Thanks. Nat.

Since I have some MET and CYT in the protein, could I try to supply their
sulfur as the initial anomalous scatters?

As for the anomalous isomorphous difference map, would it be useful I
compare the datasets acquired at 1A wavelength and at the Br absorption
peak (~0.92A)?

Appreciate your help


On Mon, Aug 25, 2014 at 5:08 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Sun, Aug 24, 2014 at 6:46 AM, CPMAS Chen <cpmasmit at gmail.com> wrote:
>> Here is the point I am not clear. If I am using phenix.refine to generate
>> LLG map, how do I pick the anomalous group since I have not placed them in
>> the model yet?
> You can't.  The LLG map only becomes really useful once you have some
> anomalous scatterers placed and refined - this is how Phaser substructure
> completion works.  If your molecules have no other significant anomalous
> scatterers other than the expected Br, the LLG map won't do you much good.
>> By the way, when I choose ion_placement and specify Br, the result comes
>> with no Br.
> Not too surprising, since the code is tuned to look for ions, not part of
> a covalent molecule, and halides also tend to bond non-specifically and we
> haven't figured out how to deal with that yet.
> I want to find whether the Br-containing ligand is seen in my protein
>> which I have a high resolution structure available.
>> I have data collected at Br wavelength, peak or higher position.
>> Phenix.xtriage reported that the anomalous signal is present to about 4A.
>> However, both AutoSol or MR-SAD cannot identify the Br position. Simply
>> say, AutoSol or MR-SAD can not generate any solution. Well, of course, the
>> simple answer would be that there is no such ligand cocrystallized.
> The simplest explanation is that you just don't have enough anomalous
> signal to determine the substructure, which can be true even if your ligand
> is bound.  Running experimental phasing to figure this out is unnecessary
> and time-consuming.
> Anyway, I am trying to see if the anomalous difference map or
>> LLG(generated by phenix.maps, this would be the initial one I assume) can
>> tell me anything more useful.
>> So, my question on this topic would be what is a better way you guys
>> would recommend to identify these Br-ligands? By the way, I did have the
>> native datasets for the same protein with ligand.
> I think in this case I would start with the simple anomalous difference
> map.  If you run phenix.find_peaks_holes (it's in the GUI, of course) and
> give anomalous data as input, it can pick out the highest peaks in the
> anomalous map.  If the ligand really is bound and the Br site is ordered I
> would expect this to be detectable.  Another alternative is to compute an
> anomalous isomorphous difference map between a dataset collected at or
> above (in eV) the Br peak, and a dataset collected below the peak.  This
> will allow you to visualize the wavelength-dependent difference in
> anomalous scattering, and it's going to be specific for elements with
> absorption edges within that energy range.  But I really don't think this
> should be necessary to answer your question.
> -Nat



Charles Chen

Research Associate

University of Pittsburgh School of Medicine

Department of Anesthesiology

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